biography

Data models for experimental subject biographies

Classes:

`Enclosure`	Where does the subject live?
`Breeding`	Information about the breeding conditions of the subject
`Gene`	An individual (trans)gene that an animal may have.
`Genotype`	Genotyping information, information about a subject's background and (potentially multiple) `Gene` s of interest
`Baselines`	Baseline health measurements for animal care regulation.
`Biography`	The combined biographical, health, genetic, and other details that define an experimental subject.

SEX(*args, **kwargs)

(F)emale
(M)ale,
(U)nknown,
(O)ther.

We are following the Neurodata Without Borders suggestions here, but note that these are not prescriptive and will be happily expanded whenever needed.

alias of Literal[‘F’, ‘M’, ‘U’, ‘O’]

pydantic model Enclosure[source]

Bases: autopilot.data.modeling.base.Data

Where does the subject live?

Show JSON schema

{
   "title": "Enclosure",
   "description": "Where does the subject live?",
   "type": "object",
   "properties": {
      "box": {
         "title": "Box",
         "description": "The number or name of the box this subject lives in, if any",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "integer"
            }
         ]
      },
      "building": {
         "title": "Building",
         "description": "The name of the building that the subject is housed in",
         "type": "string"
      },
      "room": {
         "title": "Room",
         "description": "The room number that the animal is housed in",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "integer"
            }
         ]
      }
   }
}

Fields

box (Optional[Union[str, int]])
building (Optional[str])
room (Optional[Union[str, int]])

field box: Optional[Union[str, int]] = None: The number or name of the box this subject lives in, if any

field building: Optional[str] = None: The name of the building that the subject is housed in

field room: Optional[Union[str, int]] = None: The room number that the animal is housed in

pydantic model Breeding[source]

Bases: autopilot.data.modeling.base.Data

Information about the breeding conditions of the subject

Show JSON schema

{
   "title": "Breeding",
   "description": "Information about the breeding conditions of the subject",
   "type": "object",
   "properties": {
      "parents": {
         "title": "Parents",
         "description": "The IDs of the parents of this subject, if any",
         "type": "array",
         "items": {
            "type": "string"
         }
      },
      "litter": {
         "title": "Litter",
         "description": "The identifying number or tag of the litter this subject was born in",
         "anyOf": [
            {
               "type": "string"
            },
            {
               "type": "integer"
            }
         ]
      }
   },
   "required": [
      "parents",
      "litter"
   ]
}

Fields

litter (Union[str, int])
parents (List[str])

field parents: List[str] [Required]: The IDs of the parents of this subject, if any

field litter: Union[str, int] [Required]: The identifying number or tag of the litter this subject was born in

pydantic model Gene[source]

Bases: autopilot.data.modeling.base.Data

An individual (trans)gene that an animal may have.

I am not a geneticist, lmk what this should look like

Show JSON schema

{
   "title": "Gene",
   "description": "An individual (trans)gene that an animal may have.\n\nI am not a geneticist, lmk what this should look like",
   "type": "object",
   "properties": {
      "name": {
         "title": "Name",
         "description": "The name of this gene",
         "type": "string"
      },
      "zygosity": {
         "title": "Zygosity",
         "description": "One of typing.Literal['heterozygous', 'homozygous']",
         "enum": [
            "heterozygous",
            "homozygous"
         ],
         "type": "string"
      }
   },
   "required": [
      "name"
   ]
}

Fields

name (str)
zygosity (Literal['heterozygous', 'homozygous'])

field name: str [Required]: The name of this gene

field zygosity: Literal['heterozygous', 'homozygous'] = None: One of typing.Literal[‘heterozygous’, ‘homozygous’]

pydantic model Genotype[source]

Bases: autopilot.data.modeling.base.Data

Genotyping information, information about a subject’s background and (potentially multiple) Gene s of interest

Todo

Call Jax’s API to get a list of available strain names

Show JSON schema

{
   "title": "Genotype",
   "description": "Genotyping information, information about a subject's background and (potentially multiple) :class:`.Gene` s of interest\n\n.. todo::\n\n    Call Jax's API to get a list of available strain names",
   "type": "object",
   "properties": {
      "strain": {
         "title": "Strain",
         "description": "The strain or background line of this subject, if any",
         "type": "string"
      },
      "genes": {
         "title": "Genes",
         "description": "A list of any transgenes that this animal has",
         "type": "array",
         "items": {
            "$ref": "#/definitions/Gene"
         }
      }
   },
   "definitions": {
      "Gene": {
         "title": "Gene",
         "description": "An individual (trans)gene that an animal may have.\n\nI am not a geneticist, lmk what this should look like",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "description": "The name of this gene",
               "type": "string"
            },
            "zygosity": {
               "title": "Zygosity",
               "description": "One of typing.Literal['heterozygous', 'homozygous']",
               "enum": [
                  "heterozygous",
                  "homozygous"
               ],
               "type": "string"
            }
         },
         "required": [
            "name"
         ]
      }
   }
}

Fields

genes (Optional[List[autopilot.data.models.biography.Gene]])
strain (Optional[str])

field strain: Optional[str] = None: The strain or background line of this subject, if any

field genes: Optional[List[autopilot.data.models.biography.Gene]] = None: A list of any transgenes that this animal has

pydantic model Baselines[source]

Bases: autopilot.data.modeling.base.Data

Baseline health measurements for animal care regulation. In the future this will be integrated with a TrialManager class to titrate trials to ensure experimental subjects remain healthy.

Show JSON schema

{
   "title": "Baselines",
   "description": "Baseline health measurements for animal care regulation. In the future this\nwill be integrated with a TrialManager class to titrate trials to ensure experimental\nsubjects remain healthy.",
   "type": "object",
   "properties": {
      "mass": {
         "title": "Mass",
         "description": "Mass (grams) of the animal before any experimental manipulation",
         "type": "number"
      },
      "minimum_pct": {
         "title": "Minimum Pct",
         "description": "The proportion (0-1) of the baseline mass that the animal is not allowed to fall under",
         "type": "number"
      }
   }
}

Fields

mass (Optional[autopilot.data.units.base.Mass])
minimum_pct (Optional[float])

field mass: Optional[autopilot.data.units.base.Mass] = None: Mass (grams) of the animal before any experimental manipulation

field minimum_pct: Optional[float] = None: The proportion (0-1) of the baseline mass that the animal is not allowed to fall under

property minimum_mass: float: The minimum mass (g), computed as mass * minimum_pct

pydantic model Biography[source]

Bases: autopilot.data.modeling.base.Attributes

The combined biographical, health, genetic, and other details that define an experimental subject.

This is stored within the /info node in a typical Subject file as metadata attributes, and accessible from Subject.info

Development Goals

Interface with the NWB biographical information schema.

Show JSON schema

{
   "title": "Biography",
   "description": "The combined biographical, health, genetic, and other details that define an experimental subject.\n\nThis is stored within the ``/info`` node in a typical :class:`.Subject` file as\nmetadata attributes, and accessible from :attr:`.Subject.info`\n\n**Development Goals**\n\n- Interface with the NWB biographical information schema.",
   "type": "object",
   "properties": {
      "id": {
         "title": "Id",
         "description": "The indentifying string, name, subject_id, etc. for this subject. This value is also used to name the related Subject file, like {id}.h5, so these are typically expected to be unique. If None is provided, a uuid.uuid4() will be generated (which will be ugly so you probably want to give an id).",
         "type": "string"
      },
      "start_date": {
         "title": "Start Date",
         "description": "The date that this subject file was created. Not that this is not necessarily the date that the subject began training, which is more reliably determined from the timestamps within the data. If none is provided, generated from current time.",
         "type": "string",
         "format": "date-time"
      },
      "dob": {
         "title": "Dob",
         "description": "The subject's date of birth. A datetime is allowed, but hours and minutes are typically not reliable. A time of midnight formally indicates that the hour and minute is not precise.",
         "type": "string",
         "format": "date-time"
      },
      "sex": {
         "title": "Sex",
         "description": "Sex of the subject, one of typing.Literal['F', 'M', 'U', 'O']. See :data:`.SEX`",
         "default": "U",
         "enum": [
            "F",
            "M",
            "U",
            "O"
         ],
         "type": "string"
      },
      "description": {
         "title": "Description",
         "description": "Some lengthier description of the subject, idk go hogwild.",
         "type": "string"
      },
      "tags": {
         "title": "Tags",
         "description": "Any additional key/value tags that apply to this subject. Idiosyncratic metadata can be stored here, but caution should be taken to not overload this field and instead extend the Biography class because these values will not be included in any resulting schema.",
         "type": "object"
      },
      "species": {
         "title": "Species",
         "description": "Species of subject, no recommendation common vs. latin names, but will be integrated with linked data schemas in the future",
         "type": "string"
      },
      "breeding": {
         "$ref": "#/definitions/Breeding"
      },
      "enclosure": {
         "$ref": "#/definitions/Enclosure"
      },
      "baselines": {
         "$ref": "#/definitions/Baselines"
      },
      "genotype": {
         "$ref": "#/definitions/Genotype"
      }
   },
   "definitions": {
      "Breeding": {
         "title": "Breeding",
         "description": "Information about the breeding conditions of the subject",
         "type": "object",
         "properties": {
            "parents": {
               "title": "Parents",
               "description": "The IDs of the parents of this subject, if any",
               "type": "array",
               "items": {
                  "type": "string"
               }
            },
            "litter": {
               "title": "Litter",
               "description": "The identifying number or tag of the litter this subject was born in",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         },
         "required": [
            "parents",
            "litter"
         ]
      },
      "Enclosure": {
         "title": "Enclosure",
         "description": "Where does the subject live?",
         "type": "object",
         "properties": {
            "box": {
               "title": "Box",
               "description": "The number or name of the box this subject lives in, if any",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            },
            "building": {
               "title": "Building",
               "description": "The name of the building that the subject is housed in",
               "type": "string"
            },
            "room": {
               "title": "Room",
               "description": "The room number that the animal is housed in",
               "anyOf": [
                  {
                     "type": "string"
                  },
                  {
                     "type": "integer"
                  }
               ]
            }
         }
      },
      "Baselines": {
         "title": "Baselines",
         "description": "Baseline health measurements for animal care regulation. In the future this\nwill be integrated with a TrialManager class to titrate trials to ensure experimental\nsubjects remain healthy.",
         "type": "object",
         "properties": {
            "mass": {
               "title": "Mass",
               "description": "Mass (grams) of the animal before any experimental manipulation",
               "type": "number"
            },
            "minimum_pct": {
               "title": "Minimum Pct",
               "description": "The proportion (0-1) of the baseline mass that the animal is not allowed to fall under",
               "type": "number"
            }
         }
      },
      "Gene": {
         "title": "Gene",
         "description": "An individual (trans)gene that an animal may have.\n\nI am not a geneticist, lmk what this should look like",
         "type": "object",
         "properties": {
            "name": {
               "title": "Name",
               "description": "The name of this gene",
               "type": "string"
            },
            "zygosity": {
               "title": "Zygosity",
               "description": "One of typing.Literal['heterozygous', 'homozygous']",
               "enum": [
                  "heterozygous",
                  "homozygous"
               ],
               "type": "string"
            }
         },
         "required": [
            "name"
         ]
      },
      "Genotype": {
         "title": "Genotype",
         "description": "Genotyping information, information about a subject's background and (potentially multiple) :class:`.Gene` s of interest\n\n.. todo::\n\n    Call Jax's API to get a list of available strain names",
         "type": "object",
         "properties": {
            "strain": {
               "title": "Strain",
               "description": "The strain or background line of this subject, if any",
               "type": "string"
            },
            "genes": {
               "title": "Genes",
               "description": "A list of any transgenes that this animal has",
               "type": "array",
               "items": {
                  "$ref": "#/definitions/Gene"
               }
            }
         }
      }
   }
}

Fields

baselines (Optional[autopilot.data.models.biography.Baselines])
breeding (Optional[autopilot.data.models.biography.Breeding])
description (Optional[str])
dob (Optional[datetime.datetime])
enclosure (Optional[autopilot.data.models.biography.Enclosure])
genotype (Optional[autopilot.data.models.biography.Genotype])
id (str)
sex (Literal['F', 'M', 'U', 'O'])
species (Optional[str])
start_date (Optional[datetime.datetime])
tags (Optional[dict])

field id: str [Optional]: The indentifying string, name, subject_id, etc. for this subject. This value is also used to name the related Subject file, like {id}.h5, so these are typically expected to be unique. If None is provided, a uuid.uuid4() will be generated (which will be ugly so you probably want to give an id).

field start_date: Optional[datetime.datetime] [Optional]: The date that this subject file was created. Not that this is not necessarily the date that the subject began training, which is more reliably determined from the timestamps within the data. If none is provided, generated from current time.

field dob: Optional[datetime.datetime] = None: The subject’s date of birth. A datetime is allowed, but hours and minutes are typically not reliable. A time of midnight formally indicates that the hour and minute is not precise.

field sex: Literal['F', 'M', 'U', 'O'] = 'U': Sex of the subject, one of typing.Literal[‘F’, ‘M’, ‘U’, ‘O’]. See SEX

field description: Optional[str] = None: Some lengthier description of the subject, idk go hogwild.

field tags: Optional[dict] = None: Any additional key/value tags that apply to this subject. Idiosyncratic metadata can be stored here, but caution should be taken to not overload this field and instead extend the Biography class because these values will not be included in any resulting schema.

field species: Optional[str] = None: Species of subject, no recommendation common vs. latin names, but will be integrated with linked data schemas in the future

field breeding: Optional[autopilot.data.models.biography.Breeding] = None

field enclosure: Optional[autopilot.data.models.biography.Enclosure] = None

field baselines: Optional[autopilot.data.models.biography.Baselines] = None

field genotype: Optional[autopilot.data.models.biography.Genotype] = None

property age: datetime.timedelta: Difference between now and dob